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Yorodumi- PDB-5b1j: Crystal structure of the electron-transfer complex of copper nitr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b1j | ||||||
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Title | Crystal structure of the electron-transfer complex of copper nitrite reductase with a cupredoxin | ||||||
Components |
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Keywords | OXIDOREDUCTASE/ELECTRON TRANSPORT / complex / copper nitrite reductase / electron transfer / OXIDOREDUCTASE-ELECTRON TRANSPORT complex | ||||||
Function / homology | Function and homology information denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / ferroxidase activity / nitrate assimilation / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity / copper ion binding Similarity search - Function | ||||||
Biological species | Alcaligenes xylosoxydans xylosoxydans (bacteria) Hyphomicrobium denitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Nojiri, M. / Koteishi, H. / Yoneda, R. / Hira, D. | ||||||
Citation | Book title: Metalloenzymes in denitrification: Applications and Environmental impacts Journal: Metalloenzymes in denitrification: Applications and Environmental impacts Year: 2016 Title: Structure and Function of Copper Nitrite Reductase Authors: Nojiri, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b1j.cif.gz | 161.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b1j.ent.gz | 127 KB | Display | PDB format |
PDBx/mmJSON format | 5b1j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b1j_validation.pdf.gz | 442.9 KB | Display | wwPDB validaton report |
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Full document | 5b1j_full_validation.pdf.gz | 448.6 KB | Display | |
Data in XML | 5b1j_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 5b1j_validation.cif.gz | 37.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/5b1j ftp://data.pdbj.org/pub/pdb/validation_reports/b1/5b1j | HTTPS FTP |
-Related structure data
Related structure data | 1oe1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36570.527 Da / Num. of mol.: 2 / Fragment: UNP residues 25-360 / Source method: isolated from a natural source Source: (natural) Alcaligenes xylosoxydans xylosoxydans (bacteria) References: UniProt: O68601, nitrite reductase (NO-forming) #2: Protein | | Mass: 13590.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hyphomicrobium denitrificans (bacteria) / References: UniProt: A7VL37 #3: Chemical | ChemComp-CU / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.42 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, potassium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jan 25, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3→19.1 Å / Num. obs: 23931 / % possible obs: 99.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3 / % possible all: 99.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1oe1 Resolution: 3→19.1 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.908 / SU B: 15.431 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.345 Å2
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Refinement step | Cycle: 1 / Resolution: 3→19.1 Å
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Refine LS restraints |
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